Title |
Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study
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Published in |
BMC Cancer, August 2018
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DOI | 10.1186/s12885-018-4736-4 |
Pubmed ID | |
Authors |
Cecily P. Vaughn, José Luis Costa, Harriet E. Feilotter, Rosella Petraroli, Varun Bagai, Anna Maria Rachiglio, Federica Zito Marino, Bastiaan Tops, Henriette M. Kurth, Kazuko Sakai, Andrea Mafficini, Roy R. L. Bastien, Anne Reiman, Delphine Le Corre, Alexander Boag, Susan Crocker, Michel Bihl, Astrid Hirschmann, Aldo Scarpa, José Carlos Machado, Hélène Blons, Orla Sheils, Kelli Bramlett, Marjolijn J. L. Ligtenberg, Ian A. Cree, Nicola Normanno, Kazuto Nishio, Pierre Laurent-Puig |
Abstract |
Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies. This methodology enables simultaneous detection of multiple ALK, ROS1, RET, and NTRK1 gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods. |
X Demographics
Geographical breakdown
Country | Count | As % |
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France | 2 | 40% |
Italy | 1 | 20% |
Unknown | 2 | 40% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 4 | 80% |
Practitioners (doctors, other healthcare professionals) | 1 | 20% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 42 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Master | 6 | 14% |
Student > Bachelor | 5 | 12% |
Student > Doctoral Student | 4 | 10% |
Researcher | 3 | 7% |
Other | 2 | 5% |
Other | 4 | 10% |
Unknown | 18 | 43% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 8 | 19% |
Medicine and Dentistry | 4 | 10% |
Agricultural and Biological Sciences | 3 | 7% |
Computer Science | 2 | 5% |
Business, Management and Accounting | 1 | 2% |
Other | 5 | 12% |
Unknown | 19 | 45% |